Dataset DOI: 10.5061/dryad.vmcvdnd57

Overview

This repository contains the LAMMPS input script files to reproduce the biased and unbiased simulations done in the article "Thermally Activated Snap-through Transitions Controlled by Tunable Free Energy Landscape".

Description of the data and file structure

Simulation scripts are provided in the directory unbiased_simulation for unbiased runs, in the directory metadynamics_simulation for well-tempered metadynamics simulations, and in the directory hyperdynamics_simulation for hyperdynamics simulations. Under the directory metadynamics_simulation, three subdirectories 1D_ WT-MetaD, 2D_ WT-MetaD, and Infrequent-MetaD contains input scripts corresponding to 1-dimensional well-tempered metadynamics, 2-dimensional well-tempered metadynamics, and infrequent metadynamics simulations.

Files

File: Scripts.zip

Once unzipped, each directory or subdirectory contains self-sufficient input script files (and data files) for conducting molecular dynamics simulations using the LAMMPS package. in.* is the main input script file written with the LAMMPS syntax; data.* is the data file for intializing the atomistic configuration of the simulated system; CH.rebo is the force field file; *.colvars is the syntax file in compatible with the Colvars module; plumed.dat is the syntax file in compatible with PLUMED 2.9 module.

Code/software

The LAMMPS (2 Aug 2023) package patched with the Colvars module and PLUMED 2.9 is used to run the scripts.